Opened 10 months ago

Closed 10 months ago

#16566 closed defect (can't reproduce)

glTexImage2D: out of memory while drawing silhouettes

Reported by: chimerax-bug-report@… Owned by: Tom Goddard
Priority: normal Milestone:
Component: Graphics Version:
Keywords: Cc:
Blocked By: Blocking:
Notify when closed: Platform: all
Project: ChimeraX

Description 

The following bug report has been submitted:
Platform:        Windows-10-10.0.22631
ChimeraX Version: 1.7 (2023-12-19 08:36:03 UTC)
Description
(Describe the actions that caused this problem to occur here)

Log:
Startup Messages  
---  
warning | Replacing fetcher for 'pdb_nmr' and format NMRSTAR from NMRSTAR
bundle with that from NMRSTAR bundle  
  
UCSF ChimeraX version: 1.7 (2023-12-19)  
© 2016-2023 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open 1TTG

Summary of feedback from opening 1TTG fetched from pdb  
---  
warning | Atom H1 is not in the residue template for VAL /A:1  
note | Fetching compressed mmCIF 1ttg from
http://files.rcsb.org/download/1ttg.cif  
  
1ttg title:  
The three-dimensional structure of the tenth type III module of fibronectin:
an insight INTO RGD-mediated interactions [more info...]  
  
Chain information for 1ttg #1  
---  
Chain | Description | UniProt  
A | FIBRONECTIN | FINC_HUMAN 1-94  
  

> preset "overall look" "publication 1 (silhouettes)"

Using preset: Overall Look / Publication 1 (Silhouettes)  
Preset expands to these ChimeraX commands:

    
    
    set bg white
    graphics silhouettes t
    lighting depthCue f

  

> ui tool show "Show Sequence Viewer"

> sequence chain /A

Alignment identifier is 1/A  

> select :asn

28 atoms, 26 bonds, 2 residues, 1 model selected  

> select :asn, gln

45 atoms, 42 bonds, 3 residues, 1 model selected  

> show sel atoms

> open 2AVP

Summary of feedback from opening 2AVP fetched from pdb  
---  
note | Fetching compressed mmCIF 2avp from
http://files.rcsb.org/download/2avp.cif  
  
2avp title:  
Crystal structure of an 8 repeat consensus TPR superhelix [more info...]  
  
Chain information for 2avp #2  
---  
Chain | Description  
A | synthetic consensus TPR protein  
  
Non-standard residues in 2avp #2  
---  
CD — cadmium ion  
  
2avp mmCIF Assemblies  
---  
1| author_defined_assembly  
  

> select add #2

625 atoms, 613 bonds, 9 pseudobonds, 97 residues, 3 models selected  

> select #2 :asn

32 atoms, 28 bonds, 4 residues, 1 model selected  

> select #2 :asn,gln

68 atoms, 60 bonds, 8 residues, 1 model selected  

> show sel cartoons

> show sel atoms

> open 3TES

Summary of feedback from opening 3TES fetched from pdb  
---  
note | Fetching compressed mmCIF 3tes from
http://files.rcsb.org/download/3tes.cif  
  
3tes title:  
Crystal Structure of Tencon [more info...]  
  
Chain information for 3tes #3  
---  
Chain | Description  
A B C D | Tencon  
  
3tes mmCIF Assemblies  
---  
1| author_and_software_defined_assembly  
2| author_and_software_defined_assembly  
3| author_and_software_defined_assembly  
4| author_and_software_defined_assembly  
  

> select #3 :gln,asn

168 atoms, 148 bonds, 20 residues, 1 model selected  

> show sel atoms

> open 5MTM

5mtm title:  
Monobody Mb(Lck_3) bound to Lck-SH2 domain [more info...]  
  
Chain information for 5mtm #4  
---  
Chain | Description | UniProt  
A | Tyrosine-protein kinase Lck | LCK_HUMAN 3-116  
B | Monobody Mb(Lck_3) |  
  
Non-standard residues in 5mtm #4  
---  
ZN — zinc ion  
  

> hide #3 models

> hide #!2 models

> hide #1 models

> select #4/B

717 atoms, 721 bonds, 4 pseudobonds, 109 residues, 2 models selected  

> select ~sel & ##selected

866 atoms, 870 bonds, 125 residues, 1 model selected  

> hide sel cartoons

> select ~sel & ##selected

717 atoms, 721 bonds, 4 pseudobonds, 109 residues, 2 models selected  

> select #4/B :gln,asn

17 atoms, 15 bonds, 2 residues, 1 model selected  

> show sel atoms

> ui tool show "Show Sequence Viewer"

> sequence chain #4/B

Alignment identifier is 4/B  

> select #4/B:78

10 atoms, 10 bonds, 1 residue, 1 model selected  

> select #4/B:78-86

73 atoms, 75 bonds, 9 residues, 1 model selected  

> select #4/B :cys

Nothing selected  

> select #4/B:43

8 atoms, 7 bonds, 1 residue, 1 model selected  

> select #4/B:43-48

52 atoms, 55 bonds, 6 residues, 1 model selected  
An error occurred in drawing the scene. Redrawing graphics is now stopped to
avoid a continuous stream of error messages. To restart graphics use the
command "graphics restart" after changing the settings that caused the error.  
  
GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\core\updateloop.py", line 84, in draw_new_frame  
view.draw(check_for_changes = False)  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\view.py", line 188, in draw  
self._draw_scene(camera, drawings)  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\view.py", line 237, in _draw_scene  
silhouette.start_silhouette_drawing(r)  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1820, in start_silhouette_drawing  
fb = self._silhouette_framebuffer(r)  
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 1856, in _silhouette_framebuffer  
dt.initialize_depth(size, depth_compare_mode=False)  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 2982, in initialize_depth  
self.initialize_texture(size, format, iformat, tdtype, ncomp,  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3008, in initialize_texture  
GL.glTexImage2D(gl_target, 0, iformat, size[0], size[1], 0, format,  
File "src\\\latebind.pyx", line 39, in
OpenGL_accelerate.latebind.LateBind.__call__  
File "src\\\wrapper.pyx", line 318, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\wrapper.pyx", line 311, in
OpenGL_accelerate.wrapper.Wrapper.__call__  
File "src\\\errorchecker.pyx", line 58, in
OpenGL_accelerate.errorchecker._ErrorChecker.glCheckError  
OpenGL.error.GLError: GLError(  
err = 1285,  
description = b'out of memory',  
baseOperation = glTexImage2D,  
pyArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArgs = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
),  
cArguments = (  
GL_TEXTURE_2D,  
0,  
GL_DEPTH_COMPONENT24,  
1339,  
811,  
0,  
GL_DEPTH_COMPONENT,  
GL_FLOAT,  
c_void_p(None),  
)  
)  
  
Exception ignored in: <function Texture.__del__ at 0x000002406534BE20>  
Traceback (most recent call last):  
File "C:\Program Files\ChimeraX_1.7\bin\Lib\site-
packages\chimerax\graphics\opengl.py", line 3076, in __del__  
raise OpenGLError('OpenGL texture was not deleted before graphics.Texture
destroyed')  
chimerax.graphics.opengl.OpenGLError: OpenGL texture was not deleted before
graphics.Texture destroyed  
QOpenGLFramebufferObject: An undefined error has occurred: 1285  
QOpenGLFramebufferObject: Framebuffer incomplete attachment.  
[Repeated 2 time(s)]QOpenGLFramebufferObject: Framebuffer incomplete, missing
attachment.  

QQuickRenderTarget: textureId is invalid  

QQuickWindow: No render target (neither swapchain nor custom target was
provided)  

[Repeated 1 time(s)]




OpenGL version: 3.3.0 - Build 31.0.101.4953
OpenGL renderer: Intel(R) UHD Graphics 770
OpenGL vendor: Intel

Python: 3.11.2
Locale: en_US.cp1252
Qt version: PyQt6 6.3.1, Qt 6.3.1
Qt runtime version: 6.3.2
Qt platform: windows

Manufacturer: Dell Inc.
Model: OptiPlex 7400 AIO
OS: Microsoft Windows 11 Pro (Build 22631)
Memory: 34,033,360,896
MaxProcessMemory: 137,438,953,344
CPU: 20 12th Gen Intel(R) Core(TM) i7-12700
OSLanguage: en-US

Installed Packages:
    alabaster: 0.7.13
    appdirs: 1.4.4
    asttokens: 2.4.1
    Babel: 2.14.0
    backcall: 0.2.0
    beautifulsoup4: 4.11.2
    blockdiag: 3.0.0
    blosc2: 2.0.0
    build: 0.10.0
    certifi: 2023.11.17
    cftime: 1.6.3
    charset-normalizer: 3.3.2
    ChimeraX-AddCharge: 1.5.13
    ChimeraX-AddH: 2.2.5
    ChimeraX-AlignmentAlgorithms: 2.0.1
    ChimeraX-AlignmentHdrs: 3.4.1
    ChimeraX-AlignmentMatrices: 2.1
    ChimeraX-Alignments: 2.12.1
    ChimeraX-AlphaFold: 1.0
    ChimeraX-AltlocExplorer: 1.1.1
    ChimeraX-AmberInfo: 1.0
    ChimeraX-Arrays: 1.1
    ChimeraX-Atomic: 1.49.1
    ChimeraX-AtomicLibrary: 12.1.3
    ChimeraX-AtomSearch: 2.0.1
    ChimeraX-AxesPlanes: 2.3.2
    ChimeraX-BasicActions: 1.1.2
    ChimeraX-BILD: 1.0
    ChimeraX-BlastProtein: 2.1.2
    ChimeraX-BondRot: 2.0.4
    ChimeraX-BugReporter: 1.0.1
    ChimeraX-BuildStructure: 2.10.5
    ChimeraX-Bumps: 1.0
    ChimeraX-BundleBuilder: 1.2.2
    ChimeraX-ButtonPanel: 1.0.1
    ChimeraX-CageBuilder: 1.0.1
    ChimeraX-CellPack: 1.0
    ChimeraX-Centroids: 1.3.2
    ChimeraX-ChangeChains: 1.1
    ChimeraX-CheckWaters: 1.3.2
    ChimeraX-ChemGroup: 2.0.1
    ChimeraX-Clashes: 2.2.4
    ChimeraX-ColorActions: 1.0.3
    ChimeraX-ColorGlobe: 1.0
    ChimeraX-ColorKey: 1.5.5
    ChimeraX-CommandLine: 1.2.5
    ChimeraX-ConnectStructure: 2.0.1
    ChimeraX-Contacts: 1.0.1
    ChimeraX-Core: 1.7
    ChimeraX-CoreFormats: 1.2
    ChimeraX-coulombic: 1.4.2
    ChimeraX-Crosslinks: 1.0
    ChimeraX-Crystal: 1.0
    ChimeraX-CrystalContacts: 1.0.1
    ChimeraX-DataFormats: 1.2.3
    ChimeraX-Dicom: 1.2
    ChimeraX-DistMonitor: 1.4
    ChimeraX-DockPrep: 1.1.3
    ChimeraX-Dssp: 2.0
    ChimeraX-EMDB-SFF: 1.0
    ChimeraX-ESMFold: 1.0
    ChimeraX-FileHistory: 1.0.1
    ChimeraX-FunctionKey: 1.0.1
    ChimeraX-Geometry: 1.3
    ChimeraX-gltf: 1.0
    ChimeraX-Graphics: 1.1.1
    ChimeraX-Hbonds: 2.4
    ChimeraX-Help: 1.2.2
    ChimeraX-HKCage: 1.3
    ChimeraX-IHM: 1.1
    ChimeraX-ImageFormats: 1.2
    ChimeraX-IMOD: 1.0
    ChimeraX-IO: 1.0.1
    ChimeraX-ItemsInspection: 1.0.1
    ChimeraX-IUPAC: 1.0
    ChimeraX-Label: 1.1.8
    ChimeraX-ListInfo: 1.2.2
    ChimeraX-Log: 1.1.6
    ChimeraX-LookingGlass: 1.1
    ChimeraX-Maestro: 1.9.1
    ChimeraX-Map: 1.1.4
    ChimeraX-MapData: 2.0
    ChimeraX-MapEraser: 1.0.1
    ChimeraX-MapFilter: 2.0.1
    ChimeraX-MapFit: 2.0
    ChimeraX-MapSeries: 2.1.1
    ChimeraX-Markers: 1.0.1
    ChimeraX-Mask: 1.0.2
    ChimeraX-MatchMaker: 2.1.2
    ChimeraX-MCopy: 1.0
    ChimeraX-MDcrds: 2.6
    ChimeraX-MedicalToolbar: 1.0.2
    ChimeraX-Meeting: 1.0.1
    ChimeraX-MLP: 1.1.1
    ChimeraX-mmCIF: 2.12.1
    ChimeraX-MMTF: 2.2
    ChimeraX-Modeller: 1.5.13
    ChimeraX-ModelPanel: 1.4
    ChimeraX-ModelSeries: 1.0.1
    ChimeraX-Mol2: 2.0.3
    ChimeraX-Mole: 1.0
    ChimeraX-Morph: 1.0.2
    ChimeraX-MouseModes: 1.2
    ChimeraX-Movie: 1.0
    ChimeraX-Neuron: 1.0
    ChimeraX-Nifti: 1.1
    ChimeraX-NRRD: 1.1
    ChimeraX-Nucleotides: 2.0.3
    ChimeraX-OpenCommand: 1.13.1
    ChimeraX-PDB: 2.7.3
    ChimeraX-PDBBio: 1.0.1
    ChimeraX-PDBLibrary: 1.0.3
    ChimeraX-PDBMatrices: 1.0
    ChimeraX-PickBlobs: 1.0.1
    ChimeraX-Positions: 1.0
    ChimeraX-PresetMgr: 1.1
    ChimeraX-PubChem: 2.1
    ChimeraX-ReadPbonds: 1.0.1
    ChimeraX-Registration: 1.1.2
    ChimeraX-RemoteControl: 1.0
    ChimeraX-RenderByAttr: 1.1
    ChimeraX-RenumberResidues: 1.1
    ChimeraX-ResidueFit: 1.0.1
    ChimeraX-RestServer: 1.2
    ChimeraX-RNALayout: 1.0
    ChimeraX-RotamerLibMgr: 4.0
    ChimeraX-RotamerLibsDunbrack: 2.0
    ChimeraX-RotamerLibsDynameomics: 2.0
    ChimeraX-RotamerLibsRichardson: 2.0
    ChimeraX-SaveCommand: 1.5.1
    ChimeraX-SchemeMgr: 1.0
    ChimeraX-SDF: 2.0.2
    ChimeraX-Segger: 1.0
    ChimeraX-Segment: 1.0.1
    ChimeraX-SelInspector: 1.0
    ChimeraX-SeqView: 2.11
    ChimeraX-Shape: 1.0.1
    ChimeraX-Shell: 1.0.1
    ChimeraX-Shortcuts: 1.1.1
    ChimeraX-ShowSequences: 1.0.2
    ChimeraX-SideView: 1.0.1
    ChimeraX-Smiles: 2.1.2
    ChimeraX-SmoothLines: 1.0
    ChimeraX-SpaceNavigator: 1.0
    ChimeraX-StdCommands: 1.12.3
    ChimeraX-STL: 1.0.1
    ChimeraX-Storm: 1.0
    ChimeraX-StructMeasure: 1.1.2
    ChimeraX-Struts: 1.0.1
    ChimeraX-Surface: 1.0.1
    ChimeraX-SwapAA: 2.0.1
    ChimeraX-SwapRes: 2.2.2
    ChimeraX-TapeMeasure: 1.0
    ChimeraX-TaskManager: 1.0
    ChimeraX-Test: 1.0
    ChimeraX-Toolbar: 1.1.2
    ChimeraX-ToolshedUtils: 1.2.4
    ChimeraX-Topography: 1.0
    ChimeraX-ToQuest: 1.0
    ChimeraX-Tug: 1.0.1
    ChimeraX-UI: 1.33.2
    ChimeraX-uniprot: 2.3
    ChimeraX-UnitCell: 1.0.1
    ChimeraX-ViewDockX: 1.3.2
    ChimeraX-VIPERdb: 1.0
    ChimeraX-Vive: 1.1
    ChimeraX-VolumeMenu: 1.0.1
    ChimeraX-vrml: 1.0
    ChimeraX-VTK: 1.0
    ChimeraX-WavefrontOBJ: 1.0
    ChimeraX-WebCam: 1.0.2
    ChimeraX-WebServices: 1.1.3
    ChimeraX-Zone: 1.0.1
    colorama: 0.4.6
    comm: 0.2.0
    comtypes: 1.1.14
    contourpy: 1.2.0
    cxservices: 1.2.2
    cycler: 0.12.1
    Cython: 0.29.33
    debugpy: 1.8.0
    decorator: 5.1.1
    docutils: 0.19
    executing: 2.0.1
    filelock: 3.9.0
    fonttools: 4.47.0
    funcparserlib: 2.0.0a0
    glfw: 2.6.4
    grako: 3.16.5
    h5py: 3.10.0
    html2text: 2020.1.16
    idna: 3.6
    ihm: 0.38
    imagecodecs: 2023.9.18
    imagesize: 1.4.1
    ipykernel: 6.23.2
    ipython: 8.14.0
    ipython-genutils: 0.2.0
    ipywidgets: 8.1.1
    jedi: 0.18.2
    Jinja2: 3.1.2
    jupyter-client: 8.2.0
    jupyter-core: 5.5.1
    jupyterlab-widgets: 3.0.9
    kiwisolver: 1.4.5
    line-profiler: 4.0.2
    lxml: 4.9.2
    lz4: 4.3.2
    MarkupSafe: 2.1.3
    matplotlib: 3.7.2
    matplotlib-inline: 0.1.6
    msgpack: 1.0.4
    nest-asyncio: 1.5.8
    netCDF4: 1.6.2
    networkx: 3.1
    nibabel: 5.0.1
    nptyping: 2.5.0
    numexpr: 2.8.8
    numpy: 1.25.1
    openvr: 1.23.701
    packaging: 23.2
    ParmEd: 3.4.3
    parso: 0.8.3
    pep517: 0.13.0
    pickleshare: 0.7.5
    Pillow: 10.0.1
    pip: 23.0
    pkginfo: 1.9.6
    platformdirs: 4.1.0
    prompt-toolkit: 3.0.43
    psutil: 5.9.5
    pure-eval: 0.2.2
    py-cpuinfo: 9.0.0
    pycollada: 0.7.2
    pydicom: 2.3.0
    Pygments: 2.16.1
    pynrrd: 1.0.0
    PyOpenGL: 3.1.7
    PyOpenGL-accelerate: 3.1.7
    pyopenxr: 1.0.2801
    pyparsing: 3.0.9
    pyproject-hooks: 1.0.0
    PyQt6-commercial: 6.3.1
    PyQt6-Qt6: 6.3.2
    PyQt6-sip: 13.4.0
    PyQt6-WebEngine-commercial: 6.3.1
    PyQt6-WebEngine-Qt6: 6.3.2
    python-dateutil: 2.8.2
    pytz: 2023.3.post1
    pywin32: 305
    pyzmq: 25.1.2
    qtconsole: 5.4.3
    QtPy: 2.4.1
    RandomWords: 0.4.0
    requests: 2.31.0
    scipy: 1.11.1
    setuptools: 67.4.0
    sfftk-rw: 0.7.3
    six: 1.16.0
    snowballstemmer: 2.2.0
    sortedcontainers: 2.4.0
    soupsieve: 2.5
    sphinx: 6.1.3
    sphinx-autodoc-typehints: 1.22
    sphinxcontrib-applehelp: 1.0.7
    sphinxcontrib-blockdiag: 3.0.0
    sphinxcontrib-devhelp: 1.0.5
    sphinxcontrib-htmlhelp: 2.0.4
    sphinxcontrib-jsmath: 1.0.1
    sphinxcontrib-qthelp: 1.0.6
    sphinxcontrib-serializinghtml: 1.1.9
    stack-data: 0.6.3
    superqt: 0.5.0
    tables: 3.8.0
    tcia-utils: 1.5.1
    tifffile: 2023.7.18
    tinyarray: 1.2.4
    tomli: 2.0.1
    tornado: 6.4
    traitlets: 5.9.0
    typing-extensions: 4.9.0
    tzdata: 2023.3
    urllib3: 2.1.0
    wcwidth: 0.2.12
    webcolors: 1.12
    wheel: 0.38.4
    wheel-filename: 1.4.1
    widgetsnbextension: 4.0.9
    WMI: 1.5.1

Change History (2)

comment:1 by pett, 10 months ago

Component: Unassigned → Graphics
Owner: set to Tom Goddard
Platform: → all
Project: → ChimeraX
Status: new → assigned
Summary: ChimeraX bug report submission → glTexImage2D: out of memory while drawing silhouettes

comment:2 by Tom Goddard, 10 months ago

Resolution: → can't reproduce
Status: assigned → closed

Out of memory creating a texture for silhouette edge calculation. Texture size was only about 4 Mbytes. User was just looking at 3 standard PDB models. This was in ChimeraX 1.7 on Windows 10, machine has 32 GB. Possibly related to the old mmCIF memory leak bug.

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